22-28785396-C-T

Variant names:

• chr22-28785396-C-T
• rs5997403
• NM_173510.4:c.603-693C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173510.4(CCDC117):​c.603-693C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 151,922 control chromosomes in the GnomAD database, including 602 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.078 (602 hom., cov: 32)
• Consequence: CCDC117 NM_173510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 5 publications found

Genes affected

CCDC117 (HGNC:26599): (coiled-coil domain containing 117)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173510.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC117	NM_173510.4	MANE Select	c.603-693C>T		intron	N/A	NP_775781.1
	CCDC117	NM_001284263.2		c.549-693C>T		intron	N/A	NP_001271192.1
	CCDC117	NM_001284264.2		c.378-693C>T		intron	N/A	NP_001271193.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC117	ENST00000249064.9	TSL:1 MANE Select	c.603-693C>T		intron	N/A	ENSP00000249064.4
	CCDC117	ENST00000936868.1		c.720-693C>T		intron	N/A	ENSP00000606927.1
	CCDC117	ENST00000936867.1		c.603-696C>T		intron	N/A	ENSP00000606926.1

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11786 AN: 151802 Hom.: 598 Cov.: 32

Gnomad AFR AF: 0.0992

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0504

Gnomad OTH AF: 0.0723

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0777 AC: 11810 AN: 151922 Hom.: 602 Cov.: 32 AF XY: 0.0792 AC XY: 5879 AN XY: 74266

African (AFR) AF: 0.0992 AC: 4109 AN: 41422

American (AMR) AF: 0.0896 AC: 1366 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1424 AN: 5136

South Asian (SAS) AF: 0.0633 AC: 304 AN: 4806

European-Finnish (FIN) AF: 0.0722 AC: 763 AN: 10570

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0504 AC: 3424 AN: 67964

Other (OTH) AF: 0.0758 AC: 159 AN: 2098

Alfa AF: 0.0607 Hom.: 37

Bravo AF: 0.0833

Asia WGS AF: 0.175 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.53
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5997403; hg19: chr22-29181384;